Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010435.1 Corchorus olitorius cultivar O-4 contig10467, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 8337
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:7511 original size:31 final size:30

Alignment explanation


    Indices: 7476--7700  Score: 131
    Period size: 31  Copynumber: 7.5  Consensus size: 30

       7466 TATTGCTAAT

                         *                 
       7476 TGCTCAAATAAGGACCTAACGTTTGCCAAAA
          1 TGCTCAAATAAGGGCCTAACGTTT-CCAAAA

                  *       *    *      *  **
       7507 TGCTCAGATAAGGGTCTGATC-TTT-TAATT
          1 TGCTCAAATAAGGGCCT-AACGTTTCCAAAA

              *                *           
       7536 TGGTCAAATAAGGGCCTAATGTTTTCCAAAA
          1 TGCTCAAATAAGGGCCTAACG-TTTCCAAAA

                           *   *      *  **
       7567 TGCTCAAATAAGGGCATGATC-TTT-TAATT
          1 TGCTCAAATAAGGGCCT-AACGTTTCCAAAA

              *                *           
       7596 TGGTCAAATAAGGGCCTAATGTTTGCCAAAA
          1 TGCTCAAATAAGGGCCTAACGTTT-CCAAAA

                             * *      *  **
       7627 TGCTCAAATAAGGGCCCGATC-TTT-TAATT
          1 TGCTCAAATAAGGG-CCTAACGTTTCCAAAA

                          *                 
       7656 TAGC-CAAATAAGGACCTAACGTTTGCCAAAA
          1 T-GCTCAAATAAGGGCCTAACGTTT-CCAAAA

                          
       7687 TGCTCAAATAAGGG
          1 TGCTCAAATAAGGG

       7701 TCTGGCGTCG


Statistics
Matches: 137,  Mismatches: 43, Indels: 28
        0.66            0.21        0.13

Matches are distributed among these distances:
  28    6  0.04
  29   51  0.37
  30   10  0.07
  31   64  0.47
  32    6  0.04

ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29


Consensus pattern (30 bp):   
TGCTCAAATAAGGGCCTAACGTTTCCAAAA

Found at i:7547 original size:60 final size:60

Alignment explanation


    Indices: 7479--7704  Score: 346
    Period size: 60  Copynumber: 3.8  Consensus size: 60

       7469 TGCTAATTGC

                                              *                         
       7479 TCAAATAAGGACCTAACGTTTGCCAAAATGCTCAGATAAGGGTCTGATCTTTTAATTTGG
          1 TCAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGG

                      *     *    *                                       
       7539 TCAAATAAGGGCCTAATGTTTTCCAAAATGCTCAAATAAGGG-CATGATCTTTTAATTTGG
          1 TCAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGTC-TGATCTTTTAATTTGG

                      *     *                         * *             * 
       7599 TCAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTAG
          1 TCAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGG

            *                                             
       7659 CCAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTG
          1 TCAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTG

       7705 GCGTCGAAAA


Statistics
Matches: 152,  Mismatches: 12, Indels: 4
        0.90            0.07        0.02

Matches are distributed among these distances:
  59    1  0.01
  60  150  0.99
  61    1  0.01

ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30


Consensus pattern (60 bp):   
TCAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGG

Found at i:7548 original size:29 final size:29

Alignment explanation


    Indices: 7514--7668  Score: 130
    Period size: 29  Copynumber: 5.2  Consensus size: 29

       7504 AAATGCTCAG

                   *                     
       7514 ATAAGGGTCTGATCTTTTAATTTGGTCAA
          1 ATAAGGGCCTGATCTTTTAATTTGGTCAA

                      *  *        **  *    
       7543 ATAAGGGCCTAATGTTTTCCAAAATGCTCAA
          1 ATAAGGGCCTGATCTTTT--AATTTGGTCAA

                    *                    
       7574 ATAAGGGCATGATCTTTTAATTTGGTCAA
          1 ATAAGGGCCTGATCTTTTAATTTGGTCAA

                      *  *     *  **  *    
       7603 ATAAGGGCCTAATGTTTGCCAAAATGCTCAA
          1 ATAAGGGCCTGATCTTT--TAATTTGGTCAA

                     *             * *   
       7634 ATAAGGGCCCGATCTTTTAATTTAGCCAA
          1 ATAAGGGCCTGATCTTTTAATTTGGTCAA

                  
       7663 ATAAGG
          1 ATAAGG

       7669 ACCTAACGTT


Statistics
Matches: 94,  Mismatches: 28, Indels: 8
        0.72            0.22        0.06

Matches are distributed among these distances:
  29   49  0.52
  31   45  0.48

ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32


Consensus pattern (29 bp):   
ATAAGGGCCTGATCTTTTAATTTGGTCAA

Done.